Output functions and fractal dimensions in dynamical systems

We present a novel method for the calculation of the fractal dimension of boundaries in dynamical systems, which is in many cases many orders of magnitude more efficient than the uncertainty method. We call it the Output Function Evaluation (OFE) method. The OFE method is based on an efficient scheme for computing output functions, such as the escape time, on a one-dimensional portion of the phase space. We show analytically that the OFE method is much more efficient than the uncertainty method for boundaries with $D<0.5$, where $D$ is the dimension of the intersection of the boundary with a one-dimensional manifold. We apply the OFE method to a scattering system, and compare it to the uncertainty method. We use the OFE method to study the behavior of the fractal dimension as the system's dynamics undergoes a topological transition.Comment: Uses REVTEX; to be published in Phys. Rev. Let

Beyond Counting: New Perspectives on the Active IPv4 Address Space

In this study, we report on techniques and analyses that enable us to capture Internet-wide activity at individual IP address-level granularity by relying on server logs of a large commercial content delivery network (CDN) that serves close to 3 trillion HTTP requests on a daily basis. Across the whole of 2015, these logs recorded client activity involving 1.2 billion unique IPv4 addresses, the highest ever measured, in agreement with recent estimates. Monthly client IPv4 address counts showed constant growth for years prior, but since 2014, the IPv4 count has stagnated while IPv6 counts have grown. Thus, it seems we have entered an era marked by increased complexity, one in which the sole enumeration of active IPv4 addresses is of little use to characterize recent growth of the Internet as a whole. With this observation in mind, we consider new points of view in the study of global IPv4 address activity. Our analysis shows significant churn in active IPv4 addresses: the set of active IPv4 addresses varies by as much as 25% over the course of a year. Second, by looking across the active addresses in a prefix, we are able to identify and attribute activity patterns to network restructurings, user behaviors, and, in particular, various address assignment practices. Third, by combining spatio-temporal measures of address utilization with measures of traffic volume, and sampling-based estimates of relative host counts, we present novel perspectives on worldwide IPv4 address activity, including empirical observation of under-utilization in some areas, and complete utilization, or exhaustion, in others.Comment: in Proceedings of ACM IMC 201

NMR assignment of the apo-form of a Desulfovibrio gigas protein containing a novel Mo–Cu cluster

Biomol NMR Assign (2007) 1:81–83 DOI 10.1007/s12104-007-9022-3We report the 98% assignment of the apo-form of an orange protein, containing a novel Mo–Cu cluster isolated from Desulfovibrio gigas. This protein presents a region where backbone amide protons exchange fast with bulk solvent becoming undetectable. These residues were assigned using 13C-detection experiments

Energy metabolism in human pluripotent stem cells and their differentiated counterparts

Background: Human pluripotent stem cells have the ability to generate all cell types present in the adult organism, therefore harboring great potential for the in vitro study of differentiation and for the development of cell-based therapies. Nonetheless their use may prove challenging as incomplete differentiation of these cells might lead to tumoregenicity. Interestingly, many cancer types have been reported to display metabolic modifications with features that might be similar to stem cells. Understanding the metabolic properties of human pluripotent stem cells when compared to their differentiated counterparts can thus be of crucial importance. Furthermore recent data has stressed distinct features of different human pluripotent cells lines, namely when comparing embryo-derived human embryonic stem cells (hESCs) and induced pluripotent stem cells (IPSCs) reprogrammed from somatic cells. Methodology/Principal Findings: We compared the energy metabolism of hESCs, IPSCs, and their somatic counterparts. Focusing on mitochondria, we tracked organelle localization and morphology. Furthermore we performed gene expression analysis of several pathways related to the glucose metabolism, including glycolysis, the pentose phosphate pathway and the tricarboxylic acid (TCA) cycle. In addition we determined oxygen consumption rates (OCR) using a metabolic extracellular flux analyzer, as well as total intracellular ATP levels by high performance liquid chromatography (HPLC). Finally we explored the expression of key proteins involved in the regulation of glucose metabolism. Conclusions/Findings: Our results demonstrate that, although the metabolic signature of IPSCs is not identical to that of hESCs, nonetheless they cluster with hESCs rather than with their somatic counterparts. ATP levels, lactate production and OCR revealed that human pluripotent cells rely mostly on glycolysis to meet their energy demands. Furthermore, our work points to some of the strategies which human pluripotent stem cells may use to maintain high glycolytic rates, such as high levels of hexokinase II and inactive pyruvate dehydrogenase (PDH). © 2011 Varum et al

Determinação da atividade de invertase em extratos enzimáticos.

bitstream/CNPAT-2010/10231/1/Dc-108.pd

The Vampire and the FOOL

This paper presents new features recently implemented in the theorem prover Vampire, namely support for first-order logic with a first class boolean sort (FOOL) and polymorphic arrays. In addition to having a first class boolean sort, FOOL also contains if-then-else and let-in expressions. We argue that presented extensions facilitate reasoning-based program analysis, both by increasing the expressivity of first-order reasoners and by gains in efficiency

Differential mesenteric fat deposition in bovines fed on silage or concentrate is independent of glycerol membrane permeability

© The Animal Consortium 2011In the meat industry, the manipulation of fat deposition in cattle is of pivotal importance to improve production efficiency, carcass composition and ultimately meat quality. There is an increasing interest in the identification of key factors and molecular mechanisms responsible for the development of specific fat depots. This study aimed at elucidating the influence of breed and diet on adipose tissue membrane permeability and fluidity and their interplay on fat deposition in bovines. Two Portuguese autochthonous breeds, Alentejana and Barrosã, recognized as late- and early-maturing breeds, respectively, were chosen to examine the effects of breed and diet on fat deposition and on adipose membrane composition and permeability. Twenty-four male bovines from these breeds were fed on silage-based or concentrate-based diets for 11 months. Animals were slaughtered to determine their live slaughter and hot carcass weights, as well as weights of subcutaneous and visceral adipose depots. Mesenteric fat depots were excised and used to isolate adipocyte membrane vesicles where cholesterol content, fatty acid profile as well as permeability and fluidity were determined. Total accumulation of neither subcutaneous nor visceral fat was influenced by breed. In contrast, mesenteric and omental fat depots weights were higher in concentrate-fed bulls relative to silage-fed animals. Membrane fluidity and permeability to water and glycerol in mesenteric adipose tissue were found to be independent of breed and diet. Moreover, the deposition of cholesterol and unsaturated fatty acids, which may influence membrane properties, were unchanged among experimental groups. Adipose membrane lipids from the mesenteric fat depot of ruminants were rich in saturated fatty acids, and unaffected by polyunsaturated fatty acids dietary levels. Our results provide evidence against the involvement of cellular membrane permeability to glycerol on fat accumulation in mesenteric fat tissue of concentrate-fed bovines, which is consistent with the unchanged membrane lipid profile found among experimental groups.This study was supported by Fundação para a Ciência e a Tecnologia (FCT) through grant PTDC/CVT/2006/66114 and individual fellowships to Ana P. Martins (SFRH/BD/2009/65046), Ana S. H. Costa (SFRH/BD/2009/61068) and Susana V. Martins (SFRH/BPD/2009/63019). Paula A. Lopes is a researcher from the program ‘‘Ciência 2008’’ from FC

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

J Biol Inorg Chem (2011) 16:1255–1268 DOI 10.1007/s00775-011-0813-8Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C–H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results